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|
%global _empty_manifest_terminate_build 0
Name: python-bx-python
Version: 0.9.0
Release: 1
Summary: Tools for manipulating biological data, particularly multiple sequence alignments
License: MIT
URL: https://github.com/bxlab/bx-python
Source0: https://mirrors.nju.edu.cn/pypi/web/packages/b1/79/6159768ef08fc5d037c184bc964d7a79984ac99d0c076b70251c89964550/bx-python-0.9.0.tar.gz
BuildArch: noarch
Requires: python3-numpy
%description
[](https://travis-ci.org/bxlab/bx-python)
[](https://bx-python.readthedocs.io/)
# bx-python
The bx-python project is a Python library and associated set of scripts for rapid implementation of genome scale analyses. The library contains a variety of useful modules, but the particular strengths are:
* Classes for reading and working with genome-scale multiple local alignments (in MAF, AXT, and LAV formats)
* Generic data structure for indexing on disk files that contain blocks of data associated with intervals on various sequences (used, for example, to provide random access to individual alignments in huge files; optimized for use over network filesystems)
* Data structures for working with intervals on sequences
* "Binned bitsets" which act just like chromosome sized bit arrays, but lazily allocate regions and allow large blocks of all set or all unset bits to be stored compactly
* "Intersecter" for performing fast intersection tests that preserve both query and target intervals and associated annotation
## Requirements
Build currently requires liblzo, e.g. sudo apt-get install liblzo2-dev on debian/ubuntu).
## Installing
The package can be installed with pip:
```pip install bx-python```
It is available in [bioconda](https://anaconda.org/bioconda/bx-python) (recommended):
```conda install -c conda-forge -c bioconda bx-python```
It is available in [Debian](https://tracker.debian.org/pkg/python-bx) and [Ubuntu](https://packages.ubuntu.com/python3-bx):
```sudo apt install python3-bx```
Or can be built from a checkout of the repository:
```python setup.py install```
%package -n python3-bx-python
Summary: Tools for manipulating biological data, particularly multiple sequence alignments
Provides: python-bx-python
BuildRequires: python3-devel
BuildRequires: python3-setuptools
BuildRequires: python3-pip
%description -n python3-bx-python
[](https://travis-ci.org/bxlab/bx-python)
[](https://bx-python.readthedocs.io/)
# bx-python
The bx-python project is a Python library and associated set of scripts for rapid implementation of genome scale analyses. The library contains a variety of useful modules, but the particular strengths are:
* Classes for reading and working with genome-scale multiple local alignments (in MAF, AXT, and LAV formats)
* Generic data structure for indexing on disk files that contain blocks of data associated with intervals on various sequences (used, for example, to provide random access to individual alignments in huge files; optimized for use over network filesystems)
* Data structures for working with intervals on sequences
* "Binned bitsets" which act just like chromosome sized bit arrays, but lazily allocate regions and allow large blocks of all set or all unset bits to be stored compactly
* "Intersecter" for performing fast intersection tests that preserve both query and target intervals and associated annotation
## Requirements
Build currently requires liblzo, e.g. sudo apt-get install liblzo2-dev on debian/ubuntu).
## Installing
The package can be installed with pip:
```pip install bx-python```
It is available in [bioconda](https://anaconda.org/bioconda/bx-python) (recommended):
```conda install -c conda-forge -c bioconda bx-python```
It is available in [Debian](https://tracker.debian.org/pkg/python-bx) and [Ubuntu](https://packages.ubuntu.com/python3-bx):
```sudo apt install python3-bx```
Or can be built from a checkout of the repository:
```python setup.py install```
%package help
Summary: Development documents and examples for bx-python
Provides: python3-bx-python-doc
%description help
[](https://travis-ci.org/bxlab/bx-python)
[](https://bx-python.readthedocs.io/)
# bx-python
The bx-python project is a Python library and associated set of scripts for rapid implementation of genome scale analyses. The library contains a variety of useful modules, but the particular strengths are:
* Classes for reading and working with genome-scale multiple local alignments (in MAF, AXT, and LAV formats)
* Generic data structure for indexing on disk files that contain blocks of data associated with intervals on various sequences (used, for example, to provide random access to individual alignments in huge files; optimized for use over network filesystems)
* Data structures for working with intervals on sequences
* "Binned bitsets" which act just like chromosome sized bit arrays, but lazily allocate regions and allow large blocks of all set or all unset bits to be stored compactly
* "Intersecter" for performing fast intersection tests that preserve both query and target intervals and associated annotation
## Requirements
Build currently requires liblzo, e.g. sudo apt-get install liblzo2-dev on debian/ubuntu).
## Installing
The package can be installed with pip:
```pip install bx-python```
It is available in [bioconda](https://anaconda.org/bioconda/bx-python) (recommended):
```conda install -c conda-forge -c bioconda bx-python```
It is available in [Debian](https://tracker.debian.org/pkg/python-bx) and [Ubuntu](https://packages.ubuntu.com/python3-bx):
```sudo apt install python3-bx```
Or can be built from a checkout of the repository:
```python setup.py install```
%prep
%autosetup -n bx-python-0.9.0
%build
%py3_build
%install
%py3_install
install -d -m755 %{buildroot}/%{_pkgdocdir}
if [ -d doc ]; then cp -arf doc %{buildroot}/%{_pkgdocdir}; fi
if [ -d docs ]; then cp -arf docs %{buildroot}/%{_pkgdocdir}; fi
if [ -d example ]; then cp -arf example %{buildroot}/%{_pkgdocdir}; fi
if [ -d examples ]; then cp -arf examples %{buildroot}/%{_pkgdocdir}; fi
pushd %{buildroot}
if [ -d usr/lib ]; then
find usr/lib -type f -printf "/%h/%f\n" >> filelist.lst
fi
if [ -d usr/lib64 ]; then
find usr/lib64 -type f -printf "/%h/%f\n" >> filelist.lst
fi
if [ -d usr/bin ]; then
find usr/bin -type f -printf "/%h/%f\n" >> filelist.lst
fi
if [ -d usr/sbin ]; then
find usr/sbin -type f -printf "/%h/%f\n" >> filelist.lst
fi
touch doclist.lst
if [ -d usr/share/man ]; then
find usr/share/man -type f -printf "/%h/%f.gz\n" >> doclist.lst
fi
popd
mv %{buildroot}/filelist.lst .
mv %{buildroot}/doclist.lst .
%files -n python3-bx-python -f filelist.lst
%dir %{python3_sitelib}/*
%files help -f doclist.lst
%{_docdir}/*
%changelog
* Sun Apr 23 2023 Python_Bot <Python_Bot@openeuler.org> - 0.9.0-1
- Package Spec generated
|
